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Public spending watchdog the National Audit Office will criticise the world's biggest civil IT programme in its long-awaited report due to be published this summer.

John Bourn, the NAO's comptroller and auditor general, has revealed that his report will say that the NHS's £6.2bn national programme for IT (NPfIT) has failed to win the hearts and minds of those who are required to use the new systems - which could mean that clinicians do not gain the full benefits of new hardware and software.

The report will also point out that parts of the NHS are having to pay for systems that are not always wanted. Some NHS staff have wanted to install their choice of systems, built to national standards, but have been expected instead to implement hardware and software that has been chosen centrally.

The criticisms in the report will conflict with a recent ministerial statement, which gave the impression that all was well with the programme.

Last month, the health minister Liam Byrne praised the progress of the NPfIT. In response to a question about the scheme by the shadow health secretary Andrew Lansley, Byrne said that it had delivered new systems to thousands of locations in the NHS. "Progress is within budget, ahead of schedule in some areas and, in the context of a 10-year programme, broadly on track in others."

But Byrne's positive comments on the programme made no reference to the results of surveys by independent companies such as Mori and Medix, which have deepened doubts about whether most clinicians will make use of new systems, although most doctors support the aims of the NPfIT.

Byrne also made no mention of delays in the delivery of core software, or concerns in trusts about whether enough money will be made available for implementing systems.

The audit office's report into the NPfIT is due to be published this summer, a year after first expected. Computer Weekly has learned that a draft report was completed by the end of last year. Publication is now being delayed by a protracted and difficult clearance process, in which Whitehall health officials can approve or query the factual content of the audit office's draft reports.

Bourn's comments on the content of the report were made in response to a question from MP Richard Bacon at a hearing last month of the Public Accounts Committee, a transcript of which has now been published.

After Bacon listed some major criticisms of the NPfIT, Bourn replied, "All the things that you say... are there [in the report]."

Bacon had compared the NPfIT to Wessex Regional Health Authority's Regional Information Systems Plan, which led to an IT-related disaster in the early 1990s. At Wessex there had been little consultation and local health officials ended up refusing to buy systems that had been chosen regionally.

Bacon said that, in the same way, trusts were effectively going to have to pick up most of the bill for local implementations of the NPfIT, without always wanting the systems being offered.

In response, Bourn said there were two main themes in his office's report. The first is on the technical expertise, the design of the systems and the contracting for it. The second has to do with "all the things that you say, which is the failure to take the people in the National Health Service with the system".

He added, "I have been very keen to make it absolutely clear that in the report that I produce it will make clear the failure to take the people in the National Health Service with them. All the things that you say - the idea of having it wished on them, the idea of having to pay for something they do not want - are there."

The report will also explain what Whitehall is doing to engage clinicians.

Connecting for Health, which is running the NPfIT, was asked by Computer Weekly whether the agency was involved in delaying the publication of the audit office's report. A spokesman said, "We have worked co-operatively with the NAO and its officials as they develop their draft. It is a matter for the NAO when the report is published." The spokesman declined to comment further.

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